normal Topology problems

  • khada
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3 years 7 months ago #4816 by khada
Topology problems was created by khada
Hey guys!

I used the martinize script to coarse grain my structure and grompp gives me following error:
Program grompp, VERSION 5.0.5
Source code file: /home/kathrin/gromacs-5.0.5/src/gromacs/gmxpreprocess/grompp.c, line: 603

Fatal error:
number of coordinates in coordinate file (transporter-cg.pdb, 3812)
does not match topology (system-vaccum.top, 4058)
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors

Ive checked the .top and coarse grained .pdb file and it appears that martinize puts in some random aminoacids into the topology.

Help! :(

Cheers,
Kathrin

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3 years 4 months ago #5211 by helgi
Replied by helgi on topic Topology problems
Hello, hello,

Without having the files it is very hard to know what is going on. Are you still having this problem? If so you could try to clean the initial .pdb (remove all unnecessary lines – martinize can get confused with some of those). If that does not work you could send us your .pdb file and we could check this for you.

Cheers,
- Helgi

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  • maryam
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1 month 2 weeks ago #8034 by maryam
Replied by maryam on topic Topology problems
Hello,
Please, I am having the same error but I thought it was because I am working with mltiple chains.

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